A big yard surrounds three sides of a very large, low building. First, take care of all the gangs of Slaughtaurs outside. You'll see a bunch of stone doors leading into the chapel; some may be open. Look for a narrow wooden door up a stairway. Pull the switch in here to open the main door to the chapel: the stone door up the stairs on the south side. In here is a large room with several rows of columns, and additional doors. The second puzzle piece is past the stone door at the far end of the room. This will be open if you pulled the first lever in the Griffin Chapel. If you've pulled the first lever in the Dragon chapel, the stone doors to either side, plus all of the remaining stone doors outside, will be open. In these areas are the remainder of the chapel, which includes the third puzzle piece.
First puzzle-piece lever[edit]
In the big first room are a couple narrow wooden doors you can open. In the one that was immediately to your right when you first entered is a small closet with the first lever. This solves one ninth of the puzzle, plus opens the left-side bars in the Griffin Chapel, and the side areas on the south side of the Dragon Chapel.
Second puzzle piece: assembly hall[edit]
Go through the stone door at the far end of the first room. In here is a corridor, plus two side rooms with stained-glass ceilings. When you step into either side room, enemies will crash through the stained glass. In the left-side room is a door to another room, with items on shelves. (If you look on the automap, you'll see evidence of a hidden door at the far end of the room. This won't open: it appears to be a carryover from when the level was in development.)
Assembly hall[edit]
Back in the main corridor, you'll be ambushed by enemies crashing through the stained glass on either side. But there are items inside the compartments. The corridor leads to a very large assembly hall with wrap-around terraces. On either side of the low end of the room are two high platforms. From the uppermost terrace, get a running start and jump to both platforms. (Hold your "jump" button and you'll clear the gap.) This solves one ninth of the puzzle, but you'll also get a great deal of company, so be on guard. This is a good place to give your #4 weapon a workout. Plus, there's a great deal of mana in the hall. That big symbol on the floor at the low end of the room will rise up out of the floor a bit and allow you to reach that compartment on the far wall with the Krater of Might.
Third puzzle piece: side rooms[edit]
There isn't anything important in the east side rooms of the chapel aside from the first lever, but there are a lot of items available. The last room can be reached from inside; it's the one with the window.
The rooms on the west side can be reached either from outside or the first room. From the inside entrance, the odd room beyond is taken up by a deep pit surrounded by a ledge. Dark Bishops below will notice you. Through the door to the right is a network of corridors, mostly forming a loop route, and many more doors. The outside entrance connects to these corridors. A puzzle-piece lever is in the rooms to the southwest of the loop; the others have a good number of items.
North room[edit]
There's some interesting mechanics in here. Note the three pedestals with the Discs of Repulsion. If you pick one up, the pedestal sinks a bit. Collect all three, and Dark Bishops will spawn out in the corridors. (If you don't need the Discs of Repulsion, you won't miss out on anything by letting them be.) Also in this room is the other side of that vestigial door in the side room past where the enemies crashed through the ceiling.
Southwest rooms and lever[edit]
In here are two small rooms in series. In the far room is the lever: pull it to solve one ninth of the puzzle. This also lowers those rounded sections of wall in the four corners, releasing enemies, plus is lowers the columns in the previous room, releasing enemies there. After taking care of them, look at the rounded sections that lowered: one is a lift that goes up to a small overhead chamber with an Icon of the Defender.